This is an R version of the particle MCMC code used in Rasmussen, D. A., Ratmann, O., & Koelle, K. (2011). Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series. PLoS computational biology, 7(8), e1002136. The raw code is written in MATLAB and obtained from the Koelle research group. I converted the raw MATLAB code into R and the file structures of raw code and mock data are preserved.
To run the particle MCMC algorithm for SIR epidemiological model with mock data, type following command in R terminal
source('main_Inference.R')